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revision 1.18 by adcroft, Tue Dec 15 21:01:56 1998 UTC revision 1.75 by jmc, Thu Jun 20 23:52:03 2002 UTC
# Line 2  $Header$ Line 2  $Header$
2    
3      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
4      ==============================      ==============================
5    o NONLIN_FRSURF: rescale gNm1 to get a better conservation with A-B
6    o change phiMin in exp1 (to agree with documentation)
7    o add new flags:
8     - T,S forcing inside/outside Adams-Bashforth
9     - turn off temp,salt advection and/or forcing
10     - for each tracer, define internal flag for multiDimAdvection & A-B
11    o monitor: change definition of KE to check conservation of Energy
12    
13    checkpoint45c_post
14    o Removed f90 comments ("!")
15    o Modified initialisations to enable exf package for MITgcm
16      (without invoking ECCO_PACKAGE).
17    o modifications to gradient check package (Martin Losch)
18      - enable centered differences
19      - modified format of standard output
20    
21    checkpoint45b_post
22    o cleaned exchange calls in cg2d
23    o Included CPP option ALLOW_AUTODIFF_MONITOR in forward_step
24    o included CPP option SINGLE_LAYER_MODE in thermodynamics
25      to configure barotropic setup (Martin Losch)
26    o moved some initialisations within bi,bj loop in dynamics
27      (TAF flow dependency)
28    o in initialise_varia, moved call packages_init_variables
29      before convective_adjustment_init
30      (corresponding adjustment of TAF tape initialisation).
31    o in calc_diffusivity/calc_viscosity extended domain to full overlap.
32    
33    checkpoint45a_post
34    o compute Rho over the whole domain (extend iMin,jMin indices)
35    o specific exchange for X-slice domain (case Ny=1)
36    o argument futureIter of S/R obcs_calc missing in exp4 & internal_wave /code
37    o solve_for_pressure : set cg2d_x to zero where OBCS are applied
38    
39    checkpoint44h_post = checkpoint45
40    o Fix to restore differentiability:
41      place at which packages_init_variables is called in
42      initialise_varia is crucial for reverse control flow.
43    o modifications in GMRedi to enable stable adjoint
44      (corresponding modif's in thermodynamics, dynamics)
45    o added missing hook for sponge layer code in external_forcing
46    o modified test cost functions
47    o storing in gad_advection (plus removal of write(0,*)!
48    o missing headers TR1.h added in convective_adjustment routines
49    o errorMessageUnit set non-equal zero in eeboot
50      (conflict on some platforms, e.g. IBM SP3)
51    o modified carbon verif.
52    
53    checkpoint44h_pre
54    o vertical grid option: allow to put the Interface at the middle between
55      2 cell-centers ; replace delZ in pkg/kpp by drF.
56    o GM Advective form: Tracers are advected using the residual transport (=
57      Euler+GM-bolus); set param GM_AdvSeparate=T to return to previous form.
58    
59    checkpoint44g_post
60    o fix surface correction term in multiDimAdvection (affects plume_on_slope
61      results) ; ifdef missing in thermodynamics.F
62    
63    checkpoint44f_pre,checkpoint44f_post
64    o added PTRACERS package
65      This allows an arbitrary number of passive tracers to be integrated
66      forward simultaneously with the dynamicaly model.
67      + Implemented so far:
68        - basic forward algorithm (time-stepping, advection, diffusion, convection)
69        - I/O and checkpointing
70        - GM/Redi  *but*  using the GM/Redi coefficient of Salt
71      + Not implemented so far:
72        - KPP
73        - OBCS
74      + No specific example supplied (yet) but global_ocean.90x40x15 has the
75        necessary data.ptracer file. Simply use -enable=ptracers and uncomment
76        line in data.pkg.
77      + This package is disabled by default since it increases storage.
78    
79    
80    o testscript: added -cleanup option
81    o Shap_filt: a) new shap_filt S/R to use no-slip BC with S2 filter
82                 b) enable to filter 2D fields.
83    
84    checkpoint44e_pre,post
85    o re-wrote convective adjustment to use pre-calculated weights
86      Affects: model/src/convective_adjustment.F, convective_adjustment_ini.F
87      Adds:    model/src/convective_weights.F, convectively_mixtracer.F
88      Original calls to convect() still in place.
89    
90    chkpt44d_pre,post
91    o added missing EXCLUDE_MONITOR flags
92    o changed "e" to "_d" in gmredi_slope_limit, gmredi_slope_psi
93      (incompatible typ in MIN/MAX expressions caused problems
94      on IBM SP3)
95    o in genmake added variable MAKEDEPEND
96      plus resetting for case SunOS
97    o added timer_stats.c routine for IBM SP3
98    o removed variables in dynamics
99    !!! I forgot to create tag chkpt44d_pre !!!
100    !!! But chkpt44d_pre = chkpt44c_post    !!!
101    
102    o real fresh water flux implemented with non-linear free-surface.
103    
104    chkpt44c_pre,post
105    o few fix (mask in shap_s2, EmPmR in external_field_load,
106      USE_NATURAL_BCS in solve_for_P);
107    o add arguments myIter & myTime to S/R obcs_calc & solve_for_P
108    
109    checkpoint44b_pre/_post
110    o merge of relevant stuff from the ecco-branch:
111      - genmake: removed $S64 overwrite for case SunOS
112      - pkg/exf: update and corrections for field swapping and obcs
113      - pkg/ecco: parameter lists for the_model_main, the_main_loop
114                  harmonized between ECCO and MITgcm
115      - pkg/autodiff: added flow directives for obcs, mdsio_gl_slice
116                      updated checkpointing_lev... lists for obcs
117      - model/src: minor changes in forward_step, plot_field
118                   added directive for divided adjoint in the_main_loop
119      - pkg/mdsio: added mdsio_gl_slice
120    
121    o check parameters & config (chkpt44a_pre,post)
122    o OBC and NonLin_FrSurf.
123    
124    checkpoint44
125    o fix bug in mom_vi_del2uv
126    o select when filters are applied ; add options to zonal_filter (data.zonfilt)
127    o gmredi: fix Pb in the adiabatic form ; add options (.e.g. Bolus advection)
128    o update AIM experiments (NCEP input files)
129    o improve and extend diagnostics (Monitor, TimeAve with NonLin-FrSurf)
130    o added some stuff for AD
131    
132    checkpoint43
133    o added two new advection tests
134    o added global 4x4 degree ocean test
135    o added test of H&S94 with free surface on cube
136    o some final mods for gradient check, adjoint,...
137    
138    checkpoint42
139      Fixed AD-related problems:
140    o Store directives up-to-date with re-arranged Adams-Bashforth
141      (mainly thermodynamics.F)
142    o New store directives for multi-dim. advection schemes
143      * new CPP flag ALLOW_MULTI_DIM_ADVECTION
144      * new common block and key passkey
145      (mainly gad_advection.F)
146    o Modified store directives for split of dynamics/thermodynamics
147      for the case ALLOW_KPP
148    o Cleaned argument list for timestep_tracer.F
149    
150    checkpoint41
151    o re-formatted/added comments in prologues of key subroutines
152      to work with protex
153    
154    checkpoint40
155    o moved calc_gs, calc_gt and calc_tr1 back to model/src
156    o added FLT (floats) package from Arne along with demo. experiment
157    o re-arranged Adams-Bashforth scheme for tracers to allow easier
158      implementation of forward-in-time forcing terms
159    o more mods for non-linear free-surface including new variable
160    o modified multi-dim method to work on cube
161    o bug fix in KPP (from DM)
162    
163    checkpoint40pre9
164    o added DST advection schemes
165    o fix MPI bug on SGI's
166    o modifications for non-linear free-surface
167    o fixed conditionals for fixed flow/passive tracer only mode
168    o added tension/strain form of stress tensor
169    o changes to commenting of arguments for TAF/TAMC
170    o added/updated many matlab scripts
171    o added multi-dimensional advection method for tracers
172      
173    checkpoint40pre8
174    o new package rw/
175      Added method for dumping intermediate local arrays:
176      mdsio_writetile - same as mdsio_writefield except works from inside
177                        bi,bj loop
178      mdsio_writelocal - same as mdsio_writetile except works for local
179                         arrays
180      write_local_r? - higher-level wrapper for mdsio_writelocal
181      Controlled by diagFreq. Defaults to zero (ie. no dumps)
182      Example given at end of mom_vecinv.F that dumps some local arrays.
183    o replaced calc_mom_rhs.F by mom_fluxform.F/mom_vecinc.F to
184      control flux-form versus vector invariant code.
185      Switch is runtime flag vectorInvariantMomentum (defaults to false)
186      or genmake -DISABLE ...
187    o TAMC-related update to cope with mom_fluxform.F/mom_vecinc.F
188      (additional storing is now needed for case vecinv;
189      currently nothing implemented to switch this storing off
190      in case fluxform is used since no CPP flag available).
191    
192    checkpoint40pre7
193    o bug fix in dynamics.F
194      calc_viscosity called before k=1,Nr loop.
195    o added some #ifdef's ALLOW_PASSIVE_TRACER
196    o cleaned initialisations in ctrl_map_ini
197      related to TAF
198    
199    checkpoint40pre6
200    o split dynamics into thermodynamics & dynamics
201    o corresponding split of calc_diffusivity into
202      calc_diffusivity, calc_viscosity
203      (kpp_calc_diff, kpp_calc_visc).
204    o Added diffkr, kapgm to control variables
205    o bug fix in gmredi_slope_limit for ldd97
206    
207    checkpoint40pre5
208    o proper initialization of Adams-Bashforth time stepping
209      + uses forward step for very first step of model (iter=0)
210    o re-generated *all* output since almost all output is modified by this
211      change (sorry but we've been putting this one off for about 2 years)
212      + natl_box, aim.5l_Equatorial_Channel and aim.5l_zon-ave were
213        *not* regenerated since they are already out of date and I don't
214        want to create the impression that they are suddenly working.
215    o removed KAP stuff for DEC's
216    o modified/added many .cvsignore files in */code and */input
217    o added new expt "solid-body.cs-32x32x1"
218      + this uses an alternative form of ini_curvilinear_grid.F which
219        is not necessarily any better than the current one...
220    
221    checkpoint40pre4
222    o added re-initialisations of utrans,vtrans,rtrans in
223      calc_common_factors which are crucial for TAF.
224    o extended iMin,jMin range for calc_common_factors,
225      calc_diffusivity
226    o added option ALLOW_PASSIVE_TRACER
227    o a few minor updates and fixes
228    
229    checkpoint40pre3
230    o created calc_gtr1.F for gad package
231    o split the_main_loop and re-introduced forward_step
232    o some recomputations of nIter0 for TAMC
233    
234    checkpoint40pre2
235    o Updated to latest branch of AJA, JMC
236    o Added gradient check package
237    o Added routines for passive tracer handling
238    o Added carbon sequestration sensitivity experiment
239    
240    checkpoint39
241     o Modifications and fixes to support TAMC
242       (mainly missing or wrong directives)
243     o Corrected common blocks when fooling TAMC to produce adjoint I/O
244       in addummy_in_stepping
245     o Updated verification/vero/ (bug fixes in code/, correct pickups in input/)
246     o Enabled "sliced" (xz-,yz-) exchanges, needed for obcs.
247     o Included following packages:
248       cal: calendar
249       exf: external forcing
250       ecco: essential routines to control use of cal, exf
251             (NB: this is not the full ECCO environment)
252     o disabled some packages by default in genmake
253    
254    checkpoint38
255     o see notes_c37_adj.txt
256     o corrected wrong layer index in external_forcing_t
257     o replaced the_main_loop/forward_step by the_main_loop
258     o removed forceoutput from write_state
259       (replaced criteria for initial/final state)
260     o added runtime flag for pre-C35 pickups: usePickupBeforeC35
261    
262    checkpoint37
263     o mdsio.F routine split and packaged in pkg/mdsio
264       (mdsio.F and mdsio_gl.F still exist in eesupp/src but are not
265        used unless genmake -disable=mdsio)
266     o allow a more precise surface-geopotential gradient for the atmosphere
267       taking into account the change in space of Alpha (=1/rho) at the surface.
268     o variable "etaN" (replace cg2d_x) is the surface R-anomaly [r unit]
269       (ocean: sea surface height [m] / atmos: surface pressure anomaly [Pa])
270     o Change units: Phi_Hydrostatic (=phiHyd), Phi_Surface(=cg2d_x) and
271       Phi_NonHydrostatic (=cg3d_x), all have now the dimension of a potential
272       [m2/s2] (pressure/rhoConst in the ocean ; Geo-Potential in the atmosphere).
273     o Time-Average diagnostics defined as a pseudo package "timeave".
274     o pickup files : old pickup (before c35) did not work with new code (c35
275       and after) unless activating 2 commented lines in initialise-varia.
276     o Non-Hydrostatic pickup file Pb fixed.
277     o bug with Rigid-lid version (since c35) fixed.  
278    
279    checkpoint36
280     o implement Crank-Nickelson barotropic time-stepping
281     o recover Time-Average diagnostics
282     o fix Pb in checkpoint (PR#19)
283     o AIM become a standard package ; clean unused CPP_kees
284    
285    checkpoint35
286     o subtantial rewrite of dynamics.f
287     o allows staggered time-stepping
288     o packaged obcs, aim (Atmospheric Physics), zonal_filt, shap_filt
289     o added bottom drag (linear + quadratic)
290    
291    checkpoint34
292     o Modified exchange routines for correct reverse simulation.
293     o Added verification output to comply with bug fix in impldiff.F
294       as of c33 (exp2, natl_box).
295     o Corrected store directives in dynamics.F
296     o Corrected array boundaries in impldiff.F
297     o Corrected array dimensions in gmredi.
298       Added temporary scalars to avoid storage by TAMC (gmredi, kpp).
299     o Added routine GLOBAL_SUM_INT to global_sum.F
300     o Added mdsio_gl.F for ECCO purposes.
301    
302    checkpoint33
303     o Fixed bug in lower BC in impldiff.F
304     o Fixed confusion about units of forcing arrays in FFIELDS.h
305       namely Fu,Fv,Qnet,Qsw,EmPmR:
306       - Removed verification/natl_box/code/external_fields_scale.F
307         (did not differ from that in model/src)
308       - Changed units of fu,fv,Qnet,Qsw,EmPmR back to proper units
309         (see FFIELDS.h for description)
310       - Scale fu,fv,Qnet,Qsw,EmPmR when used in external_forcing_surf.F,
311         kpp_calc.F and kpp_transport_t.F
312       - Removed model/src/external_fields_scale.F and calls to it
313       - verification/natl_box uses flux data with "atmospheric" sign so
314         a special version of external_fields_load.F is used to
315         change the data as it's read in. This way, the arrays
316         have the right units and signs at all times tha a user could
317         possibly use them.
318     o Corrected genmake to delete a temporary file during configuration
319    
320    checkpoint32
321     o Scaling of forcing fields moved from external_forcing.F to
322       external_fields_scale.F, called directly after loading fields.
323     o Surface relaxation terms added to surface tendency fields in
324       extra subroutine.
325     o impldiff.F changed to avoid storing by TAMC of huge intermediate
326       fields.
327     o Changes in GMRedi to comply with packaging structure.
328     o Modifications and bug fixes in KPP package.
329     o Verification experiment for KPP added (verification/nat_box/)
330    
331    checkpoint31
332     o Packages interface brought in line with defined standard
333       -> new routines packages_...F
334       -> changes in initialise_fixed.F, initialise_varia.F
335       -> enables initialisation interface for ECCO package
336     o Rescaling of external forcing fields immediately after read
337       (removed from external_forcing.F)
338       -> new: surface_fields_scale.F
339       -> affects ini_foorcing.F, external_fields_load.F
340     o Computation of surface tendencies before tendency updates.
341       -> new: external_forcing_surf.F
342     o Change of variable names useGMRedi, useKPP, useECCO
343     o Further changes in dynamics.F, impldiff.F for TAMC
344     o Tested for experiments 0, 2, 4.
345       - not yet tested for GMRedi.
346       - not yet tested for KPP.
347    
348    checkpoint30
349     o Updates for OBCs
350     o New experiment for test OBCs (internal_wave)
351     o New output.txt in verification/exp4/results/
352     o Updates for KPP: calculation of viscosity corrected, new variables
353       kpp_dumpFreq and kpp_taveFreq
354     o CPP'd calls to system routines for TARGET_CRAY_VECTOR (P.H.)
355       and entry for T90 in genmake
356    
357    checkpoint29
358     o packaged KPP and GM/Redi
359    
360    checkpoint28
361     o Corrected initialization of hFacMin for difference vertical coordinates
362     o Modified calculation of partial cell thickness to more robust algorithm
363     o config_summary.F: replaced write_1D_... by write_0D_...
364       read_write.F: added subroutines write_0D_...
365     o routines calc_common_factors, calc_gs, calc_gt, calc_phi_hyd, find_rho:
366       included some initialisations required for TAMC.
367     o routine calc_isoslopes: modified sqrt computation to make it
368       differentiable for zero argument.
369     o routines dynamics, impldiff:
370       included store directives and tape key computations required for TAMC.
371     o ALL TAMC related changes are between ifdef ALLOW_AUTODIFF_TAMC
372    
373    checkpoint27
374     o fixed calc_isoslopes() to so that cancellation of terms in tensor
375       formulation works properly with variable resolution.
376     o restructured the calling tree between the_model_main() and dynamics()
377     o split initialise() into initialise_fixed() and initialise_varia()
378     o introduced initialization file pSurfInitFile for free surface (cg2d_x)
379       in new routine ini_psurf()
380    
381    checkpoint26
382     o moved some #ifdef in optional routines to encompass everything
383       except the argument declarations. This was using up some memory.
384     o fixed macros like _ADT to work with both versions of Linux cpp
385     o cleaned up some unused and uninitialized variables
386       (helps when debugging with strict compile options)
387     o split up CPP_EEOPTIONS.h into options and macros
388       (macros are now in eesupp/inc/CPP_EEMACROS.h)
389     o patch for 2 processor JAM mode
390    
391    checkpoint25
392     o updates for OBCs and NH
393     o dramatically reduced memory usage
394     o added "JAM" routines for use on Artic network
395     o parameterization of convection by implicit vertical diffusion
396     o added a diagnostic of convective index
397     o moved call to calc_divg_hat() from dynamics() to solve_for_pressure()
398       (this is was partly for OBCs and NH but also in anticipation of
399        an explicit free-surface option)
400     o initial state input files for U and V
401    
402    checkpoint24
403     o Removed some spurious "REAL"s
404     o Updated KPP to latest version from JPL
405     o Added a COS(latitude) in horizontal viscosity
406    
407    checkpoint23
408     o Added del^4 diffusion for salt and temperature
409     o Multiple minor fixes (implicit none's, arguments to global_sum, etc.)
410    
411    checkpoint22
412     o Made many small changes: implicit none, format(i5), etc...
413     o Introduced KPP mixing scheme (compiles and runs but *not* tested)
414    
415    checkpoint21
416     o Introduced new I/O package that supports direct-access records (mdsio.F)
417     o Split-up mid-level I/O routines
418     o Updated input data for experiments 0,1,2,4 and 5
419     o Finally removed the genmake.* scripts (everyone seems happy with genmake)
420    
421    checkpoint20
422     o Tidied up open-boundaries some more
423     o Added non-hydrostatic code
424     o Fixed some input data
425     o Modified MPI start-up to work in "coupled" context.
426    
427  checkpoint19  checkpoint19
428   o Tidied up directory structure for verification experiments.   o Tidied up directory structure for verification experiments.
# Line 9  checkpoint19 Line 430  checkpoint19
430   o Corrected advective terms near boundaries.   o Corrected advective terms near boundaries.
431   o Added CPP flag for "old UV" geometry and corrected spherical geometry.   o Added CPP flag for "old UV" geometry and corrected spherical geometry.
432   o Implemented free-slip/no-slip BCs and del^4 dissipation.   o Implemented free-slip/no-slip BCs and del^4 dissipation.
433   o Split default parameters out f ini_parms.F into set_defaults.F.   o Split default parameters out of ini_parms.F into set_defaults.F.
434    
435  checkpoint18  checkpoint18
436   o Further changes for optional code generation with   o Further changes for optional code generation with

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